Contacts of the helix formed by residues 607 - 619 (chain A) in PDB entry 3UGM
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 607 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLY* 5.4 3.8 - - - +
605A ASN 3.2 0.6 + - - -
606A ILE* 1.3 78.1 - - - +
608A GLY* 1.3 67.6 + - - +
609A LYS* 2.7 6.2 + - - -
610A GLN 2.8 5.0 + - - -
611A ALA* 2.8 28.4 + - - +
642A GLY* 6.5 0.4 - - - -
9B C 4.5 21.5 + - - -
10B C 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLY 5.7 0.4 + - - -
577A ALA* 4.0 15.4 - - - +
602A ILE 4.0 13.6 + - - -
603A ALA* 3.9 21.1 - - - -
605A ASN 3.4 7.9 + - - -
607A GLY* 1.3 74.7 - - - +
609A LYS* 1.3 55.9 + - - +
611A ALA* 4.7 0.7 - - - -
612A LEU* 2.9 40.5 + - - +
9B C 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLN* 4.1 29.4 - - + +
577A ALA* 4.4 4.6 - - - +
580A THR* 3.7 29.4 - - + +
607A GLY 2.7 4.8 + - - -
608A GLY* 1.3 69.6 - - - +
610A GLN* 1.3 87.7 + - + +
611A ALA 3.1 1.6 - - - -
612A LEU* 3.0 2.9 + - - +
613A ALA* 2.6 43.5 + - + +
9B C 3.5 16.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A GLY 2.8 8.0 + - - +
609A LYS* 1.3 103.7 + - - +
611A ALA* 1.3 52.6 - - - +
613A ALA* 3.5 7.7 - - - +
614A THR* 2.2 38.9 + - - -
643A LYS* 3.5 32.0 + - + +
9B C 2.9 60.5 + - - +
10B C 3.8 12.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A ILE* 4.7 17.9 - - + +
605A ASN* 6.2 0.9 - - - +
606A ILE 5.9 0.2 - - - +
607A GLY* 2.8 19.8 + - - +
608A GLY 4.4 2.0 - - - +
610A GLN* 1.3 74.7 - - - +
612A LEU* 1.3 61.5 + - - +
613A ALA 3.0 1.6 - - - -
614A THR* 3.2 5.0 + - - -
615A VAL* 2.8 31.5 + - - +
637A ALA* 4.8 6.0 - - - +
642A GLY* 3.9 30.5 - - - +
643A LYS* 4.5 0.4 - - - +
646A LEU* 4.1 2.6 - - - +
10B C 5.3 0.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A ALA 5.1 0.9 - - - +
580A THR* 4.6 7.2 - - + +
581A VAL* 4.2 31.2 - - + +
584A LEU* 3.9 23.4 - - + +
588A LEU* 4.4 16.6 - - + -
599A VAL* 4.6 8.3 - - + -
602A ILE* 3.6 45.3 - - + +
603A ALA* 4.5 14.1 - - + -
608A GLY 2.9 27.6 + - - +
609A LYS* 3.0 4.2 + - - +
611A ALA* 1.3 75.4 - - - +
613A ALA* 1.3 58.5 + - - +
615A VAL* 3.2 9.1 - - + +
616A GLN* 3.1 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A THR* 5.7 2.0 - - + -
584A LEU* 4.8 8.5 - - + -
609A LYS* 2.6 26.2 + - + +
610A GLN* 3.5 11.0 - - - +
612A LEU* 1.3 76.7 - - - +
614A THR* 1.3 60.7 + - - +
615A VAL 3.1 1.3 - - - -
616A GLN* 4.0 4.8 + - - +
617A ARG* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A GLN 2.2 27.6 + - - -
611A ALA 3.2 0.8 + - - -
613A ALA* 1.3 74.8 - - - +
615A VAL* 1.3 71.2 + - - +
617A ARG* 3.9 9.6 - - - +
618A LEU* 2.9 51.8 + - + +
643A LYS* 3.1 21.3 - - + +
646A LEU* 3.5 25.1 - - + +
647A GLU* 3.7 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A LEU* 3.0 40.2 - - + -
594A LEU* 5.6 2.2 - - + -
602A ILE* 4.8 9.6 - - + -
611A ALA 2.8 15.0 + - - +
612A LEU* 3.2 17.3 - - + +
614A THR* 1.3 81.0 - - - +
616A GLN* 1.4 72.8 + - - +
617A ARG 3.0 0.2 - - - -
619A LEU* 2.8 42.0 + - + +
633A VAL* 5.3 7.9 - - + -
634A VAL* 5.6 2.7 - - + -
637A ALA* 4.1 22.4 - - + -
646A LEU* 4.5 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584A LEU* 4.6 18.4 - - + +
587A VAL* 3.6 26.6 + - + +
588A LEU* 4.4 6.4 - - + +
591A ALA* 3.4 26.0 - - - +
592A HIS* 2.8 32.5 + - - -
612A LEU 3.1 11.3 + - - +
613A ALA* 4.0 4.0 + - - +
615A VAL* 1.4 80.2 - - + +
617A ARG* 1.3 63.4 + - - +
620A PRO* 4.3 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA 3.1 23.1 + - - +
614A THR* 3.5 12.4 - - - +
615A VAL 2.9 0.8 + - - -
616A GLN* 1.3 83.0 - - - +
618A LEU* 1.3 91.3 + - + +
619A LEU 3.4 0.7 + - - -
620A PRO* 3.5 5.5 - - - +
621A VAL* 3.5 14.0 - - - +
647A GLU* 3.3 27.5 + - - +
650A GLN* 5.4 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A THR* 2.9 42.1 + - + +
617A ARG* 1.3 100.3 - - + +
619A LEU* 1.3 65.1 + - - +
620A PRO* 3.4 1.1 - - - -
621A VAL* 3.2 29.3 + - + +
622A LEU* 3.1 31.0 - - + +
646A LEU* 4.1 18.2 - - + +
647A GLU* 4.0 16.4 - - + -
650A GLN* 4.4 27.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
592A HIS* 3.0 48.5 - - + +
594A LEU* 4.5 18.4 - - + -
615A VAL* 2.8 31.8 + - + +
616A GLN* 4.8 0.2 - - - +
618A LEU* 1.3 73.1 - - - +
620A PRO* 1.4 75.4 - - + +
622A LEU* 3.5 11.9 + - - +
623A CYS* 3.7 22.0 + - + -
630A PRO* 4.9 11.9 - - + +
633A VAL* 4.1 27.4 - - + +
634A VAL* 5.5 2.0 - - + -
646A LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il